Iron Man: Family life
by ArtemisMorningstarChase7437
Summary: This is my AU of the MCU. After the events of Avengers Civil War, Tony marries Pepper and has a son. But in the shadows a new organization has risen and threatens his family. Can the Avengers stop this new powerful enemy?


**AN: My first fanfic ever. Set after Avengers: Civil War. Infinity war never happened.**

**Disclaimer: I don't own anything of Marvel.**

Tony Stark looked out at the breathtaking evening Manhattan skyline from his office at the top floor of Stark Tower. As he sipped his favourite coffee, he took a trip down memory lane. He had spent an awesome 6 years with the love of his life, Pepper Potts, now Pepper Stark. A year after their marriage, they were blessed with a bouncing baby boy. Named after Tony's father and Pepper's uncle, Howard Morgan Stark brought joy and surprises to their life.

The adorable boy was every bit of a genius as his father. He had inherited his mother's looks along with his father's smarts and dark eyes. When Howard was two years old, he could already read. Some days, he'd help out with Tony's projects in the lab.

"Boss, Incoming call from Beautiful wife" F.R.I.D.A.Y said, as her voice brought Tony back into reality.

"Accept call." said Tony. "Hello?"

"Tony, you better come home right now or you are going to be late for the party." scolded Pepper.

"Alright, Pepper." He replied as he prepared himself to go home "Let me just finish up on Howard's present in the lab before I join you."

"Okay. Hurry up and don't be late. Love you." she said

"Love you too, Honey" Tony said and ended the call.

Tony arrived at the party not at all late and joined in the celebration of his son's fifth birthday. After the candles were blown out and most of the presents had been opened, Howard waited in anticipation to find out what his parents, more specifically what Tony, got him for his birthday. Tony handed him a tiny box wrapped in some Iron Man wrapping paper. After a moment of confusion, Howard tore of the wrapping paper and opened the box.

Inside the box was a futuristic-looking yet simple bracelet. Tony snapped it on Howard's wrist and explained how the bracelet worked.

"See this little green button here Howie? Press it and let the magic happen." explained Tony.

Curious, Howard pressed it and soon, a child-size replica of Iron Man was standing in his place. The masked opened up to reveal Howard's adorable face smiling with gleeful delight.

"Thank you, Daddy, Mommy. I love you very much" Howard exclaimed, as he started testing out his new 'toy' in front of the wide-eyed guests.

However, Pepper wasn't as pleased as Howard. After the party had ended and everyone else had gone home, she gave her husband a 'we-got-to-talk-now' look. Tony inwardly sighed as he grudgingly followed her. He wasn't looking forward to the conversation that was going to take place.

For the last couple of days, he and Pepper had been talking, though it seem more like fighting, about Howard's future. Pepper wanted to give their son a normal life and go to school like most kids. While Tony, on the other hand, disagreed and wanted his talented son to embrace his genius and be homeschooled.

"Tony, explain why you would do something like this!" Pepper shouted angrily.

"First, you want him to be alone and friendless. Now, you want him out there risking his life while I worry myself to death."

"Calm down, Pepper. Yes, I made this armor without telling you about it and it was a big mistake on my part. But, I did this for a good reason and not in the way you think. Don't tell me you are jealous that Howard got his own armor." Tony said.

"No, I am not jealous. And what else I am supposed to think? That you did it just because you have a lot of free time on your hands." argued Pepper, her voice getting louder.

Tony's temper suddenly blew at the last accusation and an argument suddenly escalated.

Unbeknownst to them, Howard heard them arguing. This wasn't the first time he heard them fighting about him. And he was very upset by it, this time especially, since it was his birthday. He wanted to do something about it and finally decided to run away.

So, little Howard used his armor and flew away into the night. To the house of America's first Avenger, Captain America.

After what she considered to be their biggest fight, Pepper went to her son's bedroom to be lost in his innocent sleeping face. Even though it seems stalkish, his presence calms her down after an argument with Tony. When she found only an empty bed in the bedroom, she started panicking. She searched every inch of the mansion but Howard was nowhere to be found. Thinking Howard might be helping his father with a project, she went down to Tony's lab. To her dismay, she only found a scowling Tony, who didn't want another fight.

"What do you want now?" said Tony in an impatient tone as he continued to work on his newest project.

"A truce. I am not here to yell at you. I can't find Howard anywhere. Have you seen him by the way?" Pepper asked, trying not to let worry take over her mind.

"No, but I can find out where he is." he replied

"F.R.I.D.A.Y, where is Howard right now?"

"Pepper, don't worry too much. The kid is always playing games that usually involve lots of hiding." Tony reassured her, despite the worry that had started building inside him.

"Boss, Howard is currently one mile north of Steve's house." the A.I informed as the holographic map was projected in front of the parents, showing their son's location.

The two shocked faces looked at each other. Both of their minds going into a state of panic worry and fear.

Pepper recovered from the shock and began panicking.

"Oh God Tony, this is all your fault. I told you the armor was a bad idea." She snapped, lashing out her worries and anger on Tony.

"Calm down, honey. Look, I am going to follow our son to Cap's house and bring him back. Later, you can put all the blame you want on me." proposed Tony.

"Just go find him and bring him back A.S.A.P." she urged.

So, Tony armored up and flew at top speed to the house of his friend.

Meanwhile, Steve Rogers put down the book he was reading when he felt a familiar boom that occurs every time Iron Man did one of his infamous landings.

"Hey Tony, what do need?" he asked as he opened the door to find a mini Iron Man.

"Whoa, did someone shrunk…?" he stopped mid-question, dumbstruck when the mask had opened up to reveal the face of Howard.

"Howard?" he said in his confusion.

"Captain America!" Howard greeted him in joy and proceeded to jump into the said person's arms.

"Hey there little buddy. What are you doing here?" asked Steve, catching the boy in his arms with his quick reflexes.

"And where are your parents?" He looked around for a glimpse of Tony's shiny armor or car.

Immediately, the boy's face scrunched up in sadness as he shook his head.

"They don't know that I am here. Mommy and Daddy were fighting about me. If I am not there anymore, Mommy and Daddy wouldn't fight anymore." He told Steve in a tearful voice.

Steve had carried him to the living room and set him down on the couch while listening to the boy's story. The former soldier was good at pep talks but comforting a five-year-old about his insecurities was a bit out of his league. Regardless, he decided to give it a try.

"Howard, let me tell you something. Your parents love you very much. I know that because the way they would do everything for you to be happy and safe. I don't know why your parents were fighting about you but I think they do it because they can't decide what makes you happy." Steve said in his comforting voice.

"Do you feel better now?" Steve asked.

Howard sniffled but nodded nonetheless.

"Pretty sure Tony is going to be here in a few minutes." Steve commented, trying to cheer up Howard.

"So buddy, what do you want to do before your dad arrives?"

Coincidently, the question was followed by a series of sharp, rapid knocking.

"Looks like Daddy Stark is here to pick you up. Are you ready to go back home?"

Howard shook his head in answer.

"Right" Steve sighed.

"Wait here and stay put while I talk with your dad."

Tony waited for what felt like eternity before the door opened, showing Steve's grim face.

"Hello Cap" Tony hesitated, worry clear on his face.

"Is he here?"

"Yeah, man. But the kid doesn't want to go home. He said he didn't want you and Pepper to fight over him so he came here." Steve replied with a look of sympathy.

"You should probably come inside and clear things up."

"Thanks Cap, for taking care of Howard" Tony patted Cap's shoulder as he passed him to the living room.

Tony approached his son as he might a wild animal, ready to bolt at the first sign of danger.

"Hey Howie, Daddy is here to say 'sorry' and give some explanations. So, no more running away from big handsome Daddy, okay?" he said in a childish voice, nearly pleading.

In the background, Steve was shaking with contained laughter that he was struggling to hold back at Tony's parenting skills. Meanwhile, Howard was looking at his usually confident father with wide eyes.

"Please Howie, come back home. Mommy and Daddy will talk with you about what is making you sad. We can eat more cake if you come back." Tony was really desperate at this point, wondering why his son wasn't saying anything.

"Wow Tony. Never knew that you are a great parent." Steve said sarcastically with an amused chuckle.

"Try being a parent. It's harder than it looks." retorted Tony before bringing back his focus on Howard.

"Howard, what do you want us to do?" Tony said, frustrated that Howard wasn't responding.

Breaking out of his silent trance, Howard finally replied in a quiet voice.

"Howard will come back home but Mommy and Daddy will stop fighting. I don't like it when you and Mommy fight."

He finished his demand with big innocent doe eyes and a pout.

Tony sighed in relief, "Alright, Daddy and Mommy will try to stop fighting when you are back home."

"Yay" Howard cheered an instant change from his previous mood.

But the sense of relief, peace and happiness that Tony feeling wasn't going to last for long. A new dark force had been rising in the shadows for a long time and had finally put their plan into action.

After Howard's mini celebration, F.R.I.D.A.Y's voice announced about a video call from Pepper. "Put her on." Tony said, wanting to tell her the good news.

The arc reactor on his chest projected a holographic image of Pepper, tied to a chair and gagged, surrounded by figures covered from head to toe in black.

"Mommy" Howard cried, suddenly afraid by his mother's state of appearance.

"This got to be some kind of joke." Tony muttered, exhausted from the day's events, from the argument with Pepper to Howard running away to this hostage situation. Another normal day in the life of Iron Man.

"F.R.I.D.A.Y, where is Pepper right now?" he asked, fearing the answer.

"She is nowhere near the house and her current location is untraceable." F.R.I.D.A.Y informed, "The security system detected a breach ten minutes ago but was hacked before it can be activated."

"Damn it, F.R.I.D.A.Y" Tony cursed. "Why didn't you tell me?"

"Sir, you told me to hold it until Howard is back home."

It was true. On the way to Steve's house, the A.I did try to inform Tony of the problem occurring at the Stark Mansion. But Tony in his panicking state of mind had told F.R.I.D.A.Y to tell him later after Howard had returned home.

A deep voice spoke, "Anthony Edward Stark, as you can see here, we have your wife as our hostage."

"If you want her to go free alive, meet us at the coordinates we send you and bring us the blueprints of the Iron Man armor and half of Starks Industries' assets."

"Wait a minute. First off, you can't have what you ask for. Secondly, who are you guys? And thirdly, don't use my full name. It makes me feel old." Tony said in his usual devil-may-care attitude.

"To answer your question, Iron Man. We are the warriors of the future. We are the next Earth's mightiest. WE ARE THE NEW AVENGERS." The voice announced triumphantly.

"And if you don't give us what we want in two hours, Mrs. Stark here will no longer be alive."

Fear gripped Tony at the thought of losing Pepper but he replied, keeping fear out of his voice, "We have a deal. I will meet you at the rendezvous point."

"Thank you for cooperating with us, Iron Man." And the video call ended.

Tony started pacing around with his 'I-am-planning-something' face. Steve looked worriedly at his friend.

"So Tony, what is our next move?" Steve asked, trying to break the tension in the room.

"Well, I am going to get Pepper back and you are going to be Howard's babysitter for tonight. Don't worry I will pay the fees." Tony replied.

"Tony, you need a better plan than that." Steve countered.

"I think it's the perfect plan. I will go get Pepper while you look after Howard and chase the bad guys away. Just in case the so-call New Avengers think I might need additional persuasion." Tony countered back.

"You aren't really going to hand the blueprints and assets over, are you?" Steve asked.

"You know me well enough to know the answer" Tony said as he armored up and became Iron Man once again.

"Take care of Howard while I am gone. By the way, his bedtime is at nine." With those words, Tony flew off.

Steve shook his head at Tony's antics and turned to faced Howard, only to find him not there sitting on the couch.

"Tony is going to kill me." swore Steve.

Tony was flying high in the sky, thinking of ways to execute his plan.

"Boss, H-1 armor is following us but trying hard to stay out of range." said F.R.I.D.A.Y.

"Looks like we found our little runaway. F.R.I.D.A.Y, connect to H-1 armor." said Tony.

Steve had texted him about the possible kink in on his 'perfect' plan.

"Connected" confirmed F.R.I.D.A.Y.

"Howard, you were supposed to stay behind with Captain America." scolded Tony. "Howard Stark, you are grounded literally after all this is over."

"But, Daddy, I want to help you to save Mommy and fight bad guys." begged Howard.

Tony sighed in frustration, torn between what to do. On one hand, he could send Howard back to Captain America but considering how stubborn his son can be, a trait he inherited from Tony, it might take some time. Time that he couldn't spare.

On the other hand, however, bringing his son into a potential battlefield isn't very appealing. The New Avengers clearly stated that only Tony have to come alone and Howard, despite being a four-… no, five-year-old, can be still considered a threat. Even if they survive, Tony would have an ear-ache from Pepper's scolding. Tony also never be able to live with himself if Howard got a scratch from the fight.

The genius Tony Stark thought it over for a long time. At last, he made his decision.

It had been an hour since the New Avengers had made their demands. At the warehouse where they were to meet, a lone figure, unarmed or unarmored, entered the warehouse.

Tony Stark clutched the briefcase he was holding to his chest as he called out,

"Hello, any future wanna-be heroes slash kidnappers in here?"

Like a cliché Hollywood scene, a light was turned on to spotlight a tied-up Pepper. Cue scene where the hero, Tony, cried out his beloved's name, "Pepper!" in distress and rushed to her, on the way, dropping the briefcase he was holding. Now, cue the cloaked and hooded villain entering the stage, emerging from where he hid in the shadows, to pick up the case that the hero had dropped.

"Well, Iron Man, I must say I am surprised that you actually obeyed and do what we want. The desperate things we do for the ones we love." the deep voice said from under the hood.

"Are you reading from a script? Because by the way you are talking, it sounds like a Hollywood movie." Tony said cockily.

"Or are you 'New Avengers' not creative enough that you are copying from movies and genius like me. Next, you are going to claim that you are Captain Blackbeard." He said, continuing to taunt the hooded figure.

The hooded figure laughed and pulled down his hood to reveal a once handsome face with its blue eyes and blond hair. The face now had a jagged scar running from his forehead, over his right eye, down to his chin. Nine more people emerged from the shadows of the warehouse. They all were different in gender, size, age and height but they had something in common. The same jagged scar the blond had, from the forehead to the chin, scarred their faces.

The blond, who appears to be the leader, replied to Tony's taunts in a menacing tone,

"For your information, Iron Man, I am the Commander, leader of the New Avengers. Although you are confident that you are going to get out of here unscathed, I am sorry to disappoint. You are not leaving this warehouse alive."

The figure chuckled in dark joy when Tony's face paled the revelation that he had walked right into a trap.

"But the deal…" Tony's voice faltered, failing him.

"Only applies to Mrs. Stark's life." The Commander explained, "If she can get out of here quick enough. Loopholes are fun, don't you agree?"

The Commander started pacing in front of the helpless couple and in typical evil mastermind fashion, started telling his plan to them,

"Now, that we have what we need, the first part of our plan is complete. The second part can now begin. Ridding the world of the troublesome Avengers, starting with you, Iron Man. You could say I am killing two birds with one stone. Next, replace them with us. The New Avengers."

At the end of his speech, the Commander removed his cloak. Beneath it, he was wearing a darker version of Captain America's suit and holding a black shield with a simple design of NA in white bold letters.

"Avengers assemble." He said with a cold smile.

Later, all the other nine people were in line behind him, their cloaks removed. They all were wearing different darker versions of the Avengers costumes and holding the replica weapons of the Avenger they represent. The Iron Man replacement was wearing an armor made of a black metallic material which unfortunately had working repulsors.

More figures emerged from the shadows, wearing the dark sinister versions costumes of other non- Avenger heroes. They all had same scar that the Commander had on their faces.

Tony's mouth went dry at the large army assembled before him. It was a show of power to make his confidence crumble at what he was going to against. He wasn't able to fight them alone but Tony has a secret trick up his sleeve.

Trying not to let them imitate him, Tony said in a brave voice,

"You won't get away with this."

"But we just did." The Commander replied as he opened the briefcase. Inside was a signed cheque for billions of dollars and a USB stick. The leader of the New Avengers held the two items in his hand and looked at Tony with a smug smile.

In a blink of an eye, faster than anyone could react, the check and the USB were nothing but ashes. The culprit was Tony wearing an Iron Man glove. Before they could even blink again, the invincible Iron Man stood in the place of Tony Stark. The composed face of the Commander broke apart and gave away to shock.

Suddenly, the doors of the warehouse burst opened and were entered by The Hulk. Following behind him was the rest of the original Avengers, with Captain America in the lead and a child-sized Iron Man. Tony looked at the shocked Commander, throwing his words back at him.

"You are right, Commander. Loopholes are fun."

**1 HOUR EARLIER…..**

"F.R.I.D.A.Y, send Cap and the other Avengers the coordinates of the rendezvous point with a message to drop everything they are doing and come there right now." Tony told the A.I. He opened up his mask and looked at Howard in the eyes.

"Look, Howie. This is the plan and I am giving you a very important job. You can follow me to where the bad guys are but don't follow me when I go inside. Instead you are going to be hiding until Daddy's friends come by. After the door is opened, go to Mommy and get out of there as fast as you can with her. Understood?" Tony instructed his son slowly, making sure Howard understood the seriousness of the situation.

Howard nodded and said,

"Don't follow Daddy inside. Hide until Daddy's friends come and open the door. Help beat up bad guys."

At Tony's stern look, Howard back-tracked sounding upset,

"No beating up bad guys. Get Mommy and get away from there."

"I know you want to be a hero. But being a hero is not just beating up bad guys and stopping their evil plans, saving people and keeping them safe is also what a hero do." Tony said, hoping to lift Howard's mood.

"So, are we going to be Mommy's heroes?" Howard asked

"Yeah, let's go be your mother's heroes." Tony replied, relieved that his family wouldn't be trapped in the crossfire. And the father and son duo flew towards the warehouse where the mother was held hostage.

**PRESENT TIME…..**

"Mommy" Howard cried as he flew to his mother and hugged her.

"Howard, you know what to do." Tony said and Howard flew out of the warehouse, carrying his Mommy away from the danger.

By this time, the Commander had recovered from his shock and smiled sardonically at the Avengers.

"Thank you, Iron Man. You just made my job easier. New Avengers, destroy them."

On the original Avengers side, Captain America corrected his doppelganger,

"No, Black. It is 'Avengers Assemble."

And all hell broke loose in the warehouse as both side charged towards the other. Laser, webs, arrows, lightning and repulsor blasts were exchanged. An aerial battle took place between those who could fly. The Avengers fought long and hard. Although they were heavily injured and exhausted, they somehow managed to get back on their feet and kept fighting. Despite their best efforts, they were still outnumbered and dropping out like files. They still failed to defeat the New Avengers.

"Captain America, the first Avenger, defeated and beaten" The Commander said, standing in front of Steve's broken form.

"The Hulk captured and restrained. Thor the Mighty God of thunder, in chains and shackles. Black Widow, not very deadly after all. Hawkeye, you shouldn't have brought arrows to a laser battle. Scarlett Witch and Vision, the two lovebirds in my cage. Falcon, the predator becomes the prey. Spiderman, kid, you should leave the hero work to the grown-ups. War Machine, this was your last battle." The Commander said with great satisfaction, taking in the broken forms of each and every Avenger.

"And finally, the invincible Iron Man, on his knees. I really wish you just cooperated peacefully, Stark, and maybe this wouldn't have happened. Because of what you did, you are the lucky winner to get front seats to witness the deaths of all your friends and family."

Horror and fear seized Tony in their vice grips. Images of Pepper's, Howard's, and all of his friends' cold, lifeless bodies, brutally killed all because of him, flashed before his eyes.

Maybe he shouldn't have gotten his friends involved. He should have taken Pepper with him to get Howard back home. Howard wouldn't have run away in the first place if he hadn't fought with Pepper. More guilty thoughts invaded Tony's mind as he lay helplessly on the ground.

"Not if his family and friends save him first." Pepper said, her voice bringing him out of his trance. She was wearing an armor, the feminine version of the Iron Man armor that was going to be Tony's wedding anniversary gift for her. Howard in his own armor was hovering next to her. Below them were most of the Avengers' allies, including S.H.I.E.L.D, Dr. Strange, the Asgardian army, Black Panther, and the Winter Soldier.

The Commander faced them with a cocky grin and said in a confident tone,

"Avengers or not, you won't be able to beat us. Ask your defeated allies, the Avengers. This is a fight you can't win. The world needs stronger heroes than these fools, who are weaklings underneath. Why are you so insisted in bringing us down?"

"Because you are not obviously smart to duplicate Tony's armor, much less protect the Earth." Nick Fury, director of the re-founded S.H.I.E.L.D, said insulting the New Avengers before adding,

"And because we are all stubborn people who never give up and always win in the end."

"For our allies and friends, the Avengers, we are willing to give our lives to help them fight and win this battle." Black Panther, the king of Wakanda said, standing in front of his powerful army.

"So, Avengers and allies, assemble." Captain America said with new-found strength and hope that came with the appearance of their friends.

Thus, the second battle between the New Avengers and the originals Avengers commenced. Only this time the tides have turned.

Despite the Avengers being heavily exhausted or injured, they fought with renewed strength at the arrival of their friends.

The Iron Man family trio was a formidable force to be reckoned with. They swooped through the enemy ranks, blasting everyone who wasn't an ally. More specifically, Howard did all that and one or both of his parents would finish the job. Eventually, the New Avengers was no match against the Avengers and their allies and the Commander was left standing alone, in the middle of the battlefield, looking defeated.

The Avengers surrounded him to prevent him from escaping. The Commander had an enraged look and his scar somehow made him look like a wild animal.

"Look at what you have done." He said, indicating to his fallen troops, his voice trembling with rage.

"The destruction you have caused so people would worship you on the pedestal that you all seem to put yourselves on. The whole world is your playground. You aren't trying to save the world. I am." He continued, slowly turning around and looking at each Avengers in the eyes. They all saw the crazed gleam in his eyes.

"You don't save the world or even protect the people living here. You are destroying it with the troubles that you brought upon it. The Avengers are weak and useless."

When he came face-to-face with Tony, the Commander launched himself on to Tony and started attacking him.

"The New Avengers would have protected the Earth better. Because of your refusal to do our bidding willingly, the Earth's greatest hope for survival is destroyed so you can continue to bask in fame and glory." The Commander babbled away, gleefully punching Tony repeatedly. The other heroes tried unsuccessfully to pull the surprisingly strong Commander off Tony. Pepper covered her son's eyes to prevent him from seeing the gruesome fight.

Fortunately Tony's helmet prevented his face from bruising and getting a broken nose. They finally managed to pull the Commander off Tony after Black Widow used her signature Black Widow's Bite to sedate the Commander.

"You okay, Tony?" Captain America asked his friend as two S.H.I.E.L.D agents dragged the unconscious Commander away somewhere, preferably a cell.

"Yeah" Tony replied as he hugged his family.

"I think this family had enough drama for a while. It's time to go home."

**A FEW DAYS LATER…..**

The Commander was a patient from a mental hospital. He was worked as a weapon manufacturer before his whole life turned upside down. His family died in a terrorist attack that the Avengers could have prevented if they weren't fighting between themselves due to the Slovakia Accords. Unable to deal with the loss, he went mad.

"Despite what he was planning to do, I feel sorry for the poor guy." Pepper said when they found out about the Commander's past.

"Not everyone gets their happy endings." Tony said as he pulled her into his arms.

They both lived up to Tony's promise to Howard and made up about the fights for their son's future. As punishment for going off alone and disobeying, Tony locked away Howard's armor for a week. Although Tony had to get a new anniversary gift, peace and happiness once again reined the Starks mansion.


End file.
